At the end of Chapter 3 ("Buddhist Epistemology and Science") in The Bodhisattva's Brain Owen Flanagan summarizes what he sees as the best position to hold about the metaphysics of consciousness:

A live option is this: keep an open mind about how conscious mental states are realized neurally, while assuming that they are. Once upon a time there was a view that there would be neat one-to-one mappings between the phenomenal and the physical. There is still some hope for identity theory for sensations. But almost no one believes that identity theory will work for more complex states. The judicious strategy is to wait and see how the mapping goes. It is likely to be very complex, with bridge principles that will need to be invented. And come what may, no nasty reductionist or materialist will be in any position to say that consciousness is an illusion or that you don't make choices (although he can say truthfully that you have no free will in the libertarian sense). That said, the best hypothesis is that the conscious mind is the most complicated biological phenomena ever studied. It is precious and beautiful and is part of the natural fabric of the universe. There is no longer any need for bewilderment, befuddlement, or mysterianism from Buddhism or any other great spiritual tradition in the face of the overwhelming evidence that all experience takes place in our embodied nervous systems in the world, the natural world, the only world there is.